Israel’s good relations with Turkey look to become another casualty of Monday’s deadly boarding of a humanitarian flotilla bound for Gaza. The only question, analysts say, is whether the rift will lead to a more radically polarized region, or force Israel to retreat from its blockade of Gaza.

“The steps that [Israel] will undertake in the coming days will be determining its position in the region,” was the ominous warning issued Wednesday by Recep Tayyip Erdogan, Turkey’s Prime Minister and the leader of its Islamic Justice and Development Party.

Mr. Erdogan told U.S. President Barack Obama in a telephone conversation that Israel was in “danger of losing its sole friend in the region.”...

“At the moment, the street and the government seem to be united in their antipathy for Israel,” said Ofra Bengio, a professor of history at Tel Aviv University and author of The Turkish-Israeli Relationship: Changing Ties of Middle Eastern Outsiders....

“It was our misfortune to play into the hands of militants,” Prof. Bengio said.

As a result, Turkey is now seen as a champion of the Palestinian cause. Its red flag, with the crescent moon and star, is flying in every Palestinian community. “It looks like the return of the Ottoman Empire,” one man said.

“There’s no doubt that Erdogan is riding high in the eyes of the public,” Prof. Bengio said. “If there’s going to be reconciliation between our countries, it will have to take place behind the scenes. The street is just too volatile.”...